Effect of variable thresholds on calculating linkage disequilibrium and population structure, using Plink 1.9

<p>The figure presented here shows how the number of LD-independent SNPs and the apparent population structure can change drastically, depending on what input thresholds are used for the calculations. The population sample consists of 220 fruit-fly (Drosophila melanogaster). Most of the population structure plots indicate four subpopulations, which on further investigation using Fst indicate that this is caused by defined trans-centromeric regions, without evidence for genotyping error, and probably reflective of historic admixture. In the plots of population structure, the number in each box indicates the number of independent SNPs which were used in the IBD calculatations. Points are coloured by order in which each fly was sequenced, and some error is noticable for the beige points in the top-right plots.</p> <p>The Plink program provides a useful method for selecting single-nucleotide polymorphisms (SNPs) which are independent of linkage disequilibrium (LD), and also of visualising the genetic relatedness between individuals in a population sample, using identity-by-descent analysis (IBD). The selection of LD-independent SNPs requires three user-specfied paramaters, alongside the genotype data: i. Window-size, in kilobases (Kb) within which all pairwise comparisons between SNPs will be made, ii. Step-size, in number of SNPs, iii. r2 threshold between any two SNPs, below which they are considered to be independent (fixed here at 0.5).</p>